bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago

10.3389/fcell.2020.577125

Development of a Metastasis-Related Immune Prognostic Model of Metastatic Colorectal Cancer and Its Usefulness to Immunotherapy
Cited by: 11
Author(s): Zhiwen Luo, Xiao Chen, Yefan Zhang, Zhen Huang, Hong Zhao, Jianjun Zhao, Zhiyu Li, Jianguo Zhou, Jianmei Liu, Jianqiang Cai, Xinyu Bi
Software Mentions: 26
Published: almost 4 years ago

10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data
Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: about 8 years ago

10.7554/eLife.43966

Unified single-cell analysis of testis gene regulation and pathology in five mouse strains
Cited by: 91
Author(s): Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon Myers, Donald F. Conrad
Software Mentions: 22
Published: over 5 years ago

10.1155/2021/8020879

Novel lncRNA Panel as for Prognosis in Esophageal Squamous Cell Carcinoma Based on ceRNA Network Mechanism
Cited by: 10
Author(s): Jin Zhang, Fei Xiao, Guangliang Qiang, Zhenrong Zhang, Qianli Ma, Hao Yang, H. Rosie Xing, Chaoyang Liang
Software Mentions: 22
Published: about 3 years ago

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago

10.1186/s13059-020-1929-3

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: almost 5 years ago

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: over 6 years ago

10.3389/fgene.2021.667936

Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections
Cited by: 9
Author(s): Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Software Mentions: 21
Published: over 3 years ago

10.3389/fimmu.2021.632333

Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic Mice
Cited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: over 3 years ago

10.1186/s13059-020-02136-7

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Cited by: 53
Author(s): Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson
Software Mentions: 21
Published: about 4 years ago

10.12688/f1000research.13577.2

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
Cited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago

10.15252/msb.20199247

<i> <scp>STAT</scp> 3 </i> ‐dependent analysis reveals <i> <scp>PDK</scp> 4 </i> as independent predictor of recurrence in prostate cancer
Cited by: 34
Author(s): Monika Oberhuber, Matteo Pecoraro, Mate Rusz, Georg Oberhuber, Maritta Wieselberg, Peter Haslinger, Elisabeth Gurnhofer, Michaela Schlederer, Tanja Limberger, Sabine Lagger, Jan Pěnčík, Petra Kodajova, Sandra Högler, Georg Stockmaier, Sandra Grund-Gröschke, Fritz Aberger, Marco Bolis, Jean-Philippe Theurillat, Robert Wiebringhaus, Theresa R. Weiss, Andrea Haitel, Marc Brehme, Wolfgang Wadsak, Johannes Griss, Thomas Mohr, Alexandra Hofer, Anton Jäger, Jürgen Pollheimer, Gerda Egger, Gunda Koellensperger, Matthias Mann, Brigitte Hantusch, Lukas Kenner
Software Mentions: 21
Published: over 4 years ago

10.1016/j.xcrm.2020.100128

The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer
Cited by: 32
Author(s): Derek J. Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C. Schürer
Software Mentions: 21
Published: about 4 years ago

10.1016/j.xcrm.2020.100096

Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
Cited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago

10.12688/f1000research.18456.1

A step-by-step guide to analyzing CAGE data using R/Bioconductor
Cited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago

10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Software Mentions: 19
Published: over 4 years ago

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

10.1084/jem.20201795

Diagnostic blood RNA profiles for human acute spinal cord injury
Cited by: 21
Author(s): Nikos Kyritsis, Abel Torres-Espín, Patrick G. Schupp, J. Russell Huie, Austin Chou, Xuan Duong Fernandez, Libby Thomas, Rachel Tsolinas, Debra D. Hemmerle, Lisa U. Pascual, Vineeta Singh, Jonathan Z. Pan, Jason F. Talbott, William D. Whetstone, John F. Burke, Anthony M DiGiorgio, Philip Weinstein, Geoffrey T. Manley, Sanjay S. Dhall, Adam R. Ferguson, Michael C. Oldham, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 19
Published: almost 4 years ago

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago

10.3389/fonc.2021.605810

A Novel Risk Factor Model Based on Glycolysis-Associated Genes for Predicting the Prognosis of Patients With Prostate Cancer
Cited by: 6
Author(s): Kaixuan Guo, Cong Lai, Juan Shi, Zhuang Tang, Cheng Liu, Kuiqing Li, Kailin Xu
Software Mentions: 18
Published: about 3 years ago

10.15252/emmm.202012640

Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor
Cited by: 7
Author(s): Maggie H. Chassé, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Software Mentions: 18
Published: almost 4 years ago

10.3389/fmicb.2019.01726

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System
Cited by: 66
Author(s): Hai-Zhen Zhu, Z.F. Zhang, Nan Zhou, Cheng‐Ying Jiang, Baojun Wang, Lei Cai, Shuang‐Jiang Liu
Software Mentions: 17
Published: over 5 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 10 years ago

10.3389/fgene.2019.00499

ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Cited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 5 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: almost 8 years ago

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago

10.1084/jem.20200920

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Cited by: 57
Author(s): Kristen E. Pauken, Osmaan Shahid, Kaitlyn A. Lagattuta, Kelly Mahuron, Jacob M. Luber, Margaret M. Lowe, Lüping Huang, Conor P. Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum, Adil Daud, Arlene H. Sharpe, Meromit Singer
Software Mentions: 17
Published: over 3 years ago

10.3389/fonc.2021.658165

Using Tumor-Infiltrating Immune Cells and a ceRNA Network Model to Construct a Prognostic Analysis Model of Thyroid Carcinoma
Cited by: 11
Author(s): Fan Zhang, Xiao‐Juan Yu, Zheyu Lin, Xichang Wang, Tengteng Gao, Di Teng, Weiping Teng
Software Mentions: 17
Published: over 3 years ago

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: almost 10 years ago

10.1186/s13059-020-02020-4

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians
Cited by: 43
Author(s): Meagan A Rubel, Arwa Abbas, Louis J. Taylor, Andrew Jesse Connell, Ceylan Tanes, Kyle Bittinger, Valantine Ngum Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 16
Published: over 4 years ago

10.12688/f1000research.16198.2

scClustViz – Single-cell RNAseq cluster assessment and visualization
Cited by: 25
Author(s): Brendan T. Innes, Gary D. Bader
Software Mentions: 16
Published: over 5 years ago

10.7554/eLife.21883

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
Cited by: 72
Author(s): Lucas T. Gray, Zizhen Yao, Thuc Nghi Nguyen, Tae Kyung Kim, Hongkui Zeng, Bosiljka Tasic
Software Mentions: 16
Published: almost 8 years ago

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago

10.1186/s13059-021-02388-x

Gene set enrichment analysis for genome-wide DNA methylation data
Cited by: 61
Author(s): Jovana Maksimovic, Alicia Oshlack, Belinda Phipson
Software Mentions: 16
Published: over 3 years ago

10.3390/life11070716

Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on Clustering
Cited by: 0
Author(s): Yunhe Liu, Aoshen Wu, Xueqing Peng, Xiaona Liu, Gang Liu, Lei Liu
Software Mentions: 15
Published: over 3 years ago

10.1038/s41598-021-88209-4

Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data
Cited by: 6
Author(s): François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jonathan D. Hill
Software Mentions: 15
Published: over 3 years ago

10.12688/f1000research.8987.2

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago

10.3389/fonc.2021.650153

Identification and Validation of a Prognostic Immune-Related Alternative Splicing Events Signature for Glioma
Cited by: 5
Author(s): Minjie Wang, Zhongqiang Zhou, Jianglin Zheng, Wenjun Xiao, Jun Zhu, Chaocai Zhang, Xueshi Jiang
Software Mentions: 15
Published: over 3 years ago

10.3390/biom10121606

A Customizable Analysis Flow in Integrative Multi-Omics
Cited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago

10.3389/fgene.2016.00163

Single-Cell Transcriptomics Bioinformatics and Computational Challenges
Cited by: 101
Author(s): Olivier Poirion, Xun Zhu, Travers Ching, Lana X. Garmire
Software Mentions: 15
Published: about 8 years ago

10.3389/fcell.2021.642724

Identification of Stemness-Related Genes for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma by Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Hongjun Guo, Siqiao Wang, Min Kyung Ju, Penghui Yan, Weiwei Sun, Zhenyu Li, Siyu Wu, Ruoyi Lin, Shuyuan Xian, Daoke Yang, Jun Wang, Zongqiang Huang
Software Mentions: 15
Published: over 3 years ago

10.1136/jitc-2020-000705

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
Cited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 years ago

10.1186/s12864-020-06856-9

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data
Cited by: 28
Author(s): Antony Kaspi, Mark Ziemann
Software Mentions: 15
Published: over 4 years ago

10.1186/s12859-017-1994-0

PIVOT: platform for interactive analysis and visualization of transcriptomics data
Cited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Software Mentions: 15
Published: almost 7 years ago

10.1186/1471-2105-16-S11-S2

VisRseq: R-based visual framework for analysis of sequencing data
Cited by: 59
Author(s): Hamid Younesy, Torsten B. Möller, Matthew C. Lorincz, Mehdi Karimi, Steven J.M. Jones
Software Mentions: 15
Published: over 9 years ago

10.1186/s12885-021-08559-0

A novel ferroptosis-related 12-gene signature predicts clinical prognosis and reveals immune relevancy in clear cell renal cell carcinoma
Cited by: 42
Author(s): Ying‐Kai Hong, Mingen Lin, Dehua Ou, Zhuangkai Huang, Peilin Shen
Software Mentions: 15
Published: over 3 years ago

10.3389/fonc.2021.560136

Screening of miRNAs as Prognostic Biomarkers for Colon Adenocarcinoma and Biological Function Analysis of Their Target Genes
Cited by: 2
Author(s): Guoliang Zheng, Guojun Zhang, Yan Zhao, Zhichao Zheng
Software Mentions: 14
Published: over 3 years ago

10.1093/bioinformatics/btw777

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Cited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago

10.1186/s13059-019-1851-8

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer
Cited by: 44
Author(s): Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth, Melissa J. Davis
Software Mentions: 14
Published: about 5 years ago

10.1186/s12859-015-0683-0

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Cited by: 172
Author(s): Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 14
Published: over 9 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.3389/fgene.2020.522125

Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles
Cited by: 11
Author(s): Nitish K. Mishra, Meng Niu, Siddesh Southekal, Prachi Bajpai, Amr Elkholy, Upender Manne, Chittibabu Guda
Software Mentions: 14
Published: about 4 years ago

10.1186/s12859-016-0971-3

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
Cited by: 20
Author(s): Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew Parnell, Stephen V. Gordon, David E. MacHugh
Software Mentions: 14
Published: over 8 years ago

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: over 4 years ago

10.1186/s12859-021-04193-6

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Cited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago

10.1186/s12859-018-2486-6

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Cited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: almost 6 years ago

10.1371/journal.ppat.1008653

Genome-wide transcriptomics identifies an early preclinical signature of prion infection
Cited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: over 4 years ago

10.1186/s12864-016-3038-y

A full-body transcriptome and proteome resource for the European common carp
Cited by: 33
Author(s): Iris Kolder, Suzanne J. van der Plas-Duivesteijn, Ge Tan, G.F. Wiegertjes, Maria Forlenza, Arzu Güler, Dmitrii Y. Travin, Minoru Nakao, Tadaaki Moritomo, Ilgiz Irnazarow, Johan T. den Dunnen, Seyed Yahya Anvar, Hans J. Jansen, Ron P. Dirks, Magnus Palmblad, Boris Lenhard, Christiaan V. Henkel, Herman P. Spaink
Software Mentions: 14
Published: about 8 years ago

10.12688/f1000research.12223.1

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
Cited by: 47
Author(s): Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe
Software Mentions: 14
Published: about 7 years ago

10.1186/s13072-020-00342-y

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Cited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: over 4 years ago

10.1038/s41598-020-80165-9

Multi-level remodelling of chromatin underlying activation of human T cells
Cited by: 23
Author(s): Naiara G. Bediaga, Hannah D. Coughlan, Timothy M. Johanson, Alexandra L. Garnham, Gaetano Naselli, Jan Schröder, Liam G. Fearnley, Esther Bandala‐Sanchez, Rhys S. Allan, Gordon K. Smyth, Leonard C. Harrison
Software Mentions: 14
Published: almost 4 years ago

10.1038/s41598-020-67753-5

Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples
Cited by: 13
Author(s): Shradha Mukherjee
Software Mentions: 14
Published: over 4 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.1111/jcmm.15705

Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade glioma
Cited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: over 4 years ago

10.1186/s12967-021-02894-3

Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responses
Cited by: 8
Author(s): Yimin Li, Shun Lü, Shubin Wang, Xinhao Peng, Jinyi Lang
Software Mentions: 14
Published: over 3 years ago

10.3389/fonc.2021.678694

A Novel Ferroptosis-Related Pathway for Regulating Immune Checkpoints in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Tianbo Xu, Xiaoping Zhang
Software Mentions: 13
Published: over 3 years ago

10.3389/fonc.2021.643104

TRIM68, PIKFYVE, and DYNLL2: The Possible Novel Autophagy- and Immunity-Associated Gene Biomarkers for Osteosarcoma Prognosis
Cited by: 10
Author(s): Jie Jiang, Dachang Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Yuanlin Yao, Wu‐Hua Chen, Hao Guo, Chong Liu, Xinli Zhan
Software Mentions: 13
Published: over 3 years ago

10.1038/srep42130

Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: almost 8 years ago

10.3389/fbioe.2020.00515

Construction of a Competitive Endogenous RNA Network for Pancreatic Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis and a Prognosis Model
Cited by: 4
Author(s): Jing Wang, Jinzhu Xiang, Xueling Li
Software Mentions: 13
Published: over 4 years ago

10.1038/s42003-021-02335-3

A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues
Cited by: 9
Author(s): José M. Ranz, Pablo M. González, Bryan D. Clifton, Nestor O. Nazario-Yepiz, Pablo Luis Hernández-Cervantes, María J. Palma-Martínez, Dulce I. Valdivia, Andrés Jiménez-Kaufman, Megan Lu, Therese A. Markow, Cei Abreu‐Goodger
Software Mentions: 13
Published: over 3 years ago

10.1186/s12864-019-5700-7

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Cited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: over 5 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: about 9 years ago

10.3389/fgene.2021.652189

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: over 3 years ago

10.1186/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: about 7 years ago

10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: almost 8 years ago

10.1186/s12859-019-3029-5

CAGEfightR: analysis of 5′-end data using R/Bioconductor
Cited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: about 5 years ago

10.3389/fonc.2021.697948

Development and Validation of a Nomogram and a Comprehensive Prognostic Analysis of an LncRNA-Associated Competitive Endogenous RNA Network Based on Immune-Related Genes for Locally Advanced Rectal Cancer With Neoadjuvant Therapy
Cited by: 2
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Tixian Xiao, Qian Liu
Software Mentions: 13
Published: over 3 years ago

10.7554/eLife.54186

Epigenetic inheritance of circadian period in clonal cells
Cited by: 12
Author(s): Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly Cox, Seung-Hee Yoo, Shao Nian Yang, Genevieve Konopka, Joseph S. Takahashi
Software Mentions: 13
Published: over 4 years ago

10.3389/fgene.2021.665888

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Cited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: over 3 years ago

10.3390/cancers13163922

Transcriptomic Profiling Reveals Novel Candidate Genes and Signalling Programs in Breast Cancer Quiescence and Dormancy
Cited by: 4
Author(s): Lewis A. Quayle, Amy Spicer, Penelope D. Ottewell, Ingunn Holen
Software Mentions: 13
Published: over 3 years ago

10.1186/s13059-020-02233-7

tidybulk: an R tidy framework for modular transcriptomic data analysis
Cited by: 22
Author(s): Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A. Doyle, Anthony T. Papenfuss
Software Mentions: 13
Published: almost 4 years ago

10.12688/f1000research.6379.2

regionReport: Interactive reports for region-level and feature-level genomic analyses
Cited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: over 8 years ago

10.1186/s13072-020-00380-6

Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling
Cited by: 7
Author(s): Jamie Grit, Benjamin K. Johnson, Patrick S. Dischinger, Curt J. Essenburg, Marie Adams, Stacy Campbell, Kai Pollard, Christine A. Pratilas, Tim Triche, Carrie R. Graveel, Matthew R. Steensma
Software Mentions: 13
Published: almost 4 years ago

10.12688/f1000research.19236.3

Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
Cited by: 11
Author(s): Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Software Mentions: 13
Published: about 5 years ago

10.7554/eLife.50087

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle
Cited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: almost 5 years ago

10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: over 4 years ago

10.1186/s13059-020-02151-8

Alignment and mapping methodology influence transcript abundance estimation
Cited by: 80
Author(s): Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Software Mentions: 13
Published: about 4 years ago

10.12688/f1000research.9501.2

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Cited by: 693
Author(s): Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni
Software Mentions: 12
Published: about 8 years ago

10.1371/journal.pone.0219698

Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns
Cited by: 11
Author(s): Alexander Platzer, Thomas Nußbaumer, Thomas Karonitsch, Josef S. Smolen, Daniel Aletaha
Software Mentions: 12
Published: over 5 years ago

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: almost 7 years ago

10.7717/peerj.9847

Prognostic implications of metabolism-associated gene signatures in colorectal cancer
Cited by: 21
Author(s): Yifei Miao, Qiutian Li, Jiangtao Wang, Wuxia Quan, Chen Li, Yuan Yang, Denghai Mi
Software Mentions: 12
Published: about 4 years ago

10.12688/f1000research.17082.2

Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk)
Cited by: 4
Author(s): Christophe D. Chabbert, Tanja Eberhart, Ilaria Guccini, Wilhelm Krek, Werner J. Kovacs
Software Mentions: 12
Published: over 5 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568